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Set initial conditions for a Simstrat simulation

Source: R/set_model_init.R
set_simstrat_init.Rd

Thin wrapper for editing the InitialConditions.dat file (temperature/ salinity) and, for a Simstrat-AED/AED2 simulation, the per-variable <var>_ini.dat override files of a Simstrat model directory in place, without needing an aeme object. Intended for a Simstrat-only workflow where a user just wants to tweak initial conditions, run the model, and load the output.

Usage

set_simstrat_init(path_simstrat, temp = NULL, salt = NULL, wq_init = NULL)

Arguments

path_simstrat

filepath; directory containing the Simstrat configuration

temp

numeric; new initial water temperature profile. Recycled to the number of depths in InitialConditions.dat. NULL (default) leaves it unchanged.

salt

numeric; new initial salinity profile, same recycling rule as temp. NULL (default) leaves it unchanged.

wq_init

named list; new initial values for water quality variables, keyed by var_aeme name, e.g. list(NIT_amm = 0.5, CHM_oxy = 300). Each value is recycled across the same depths as InitialConditions.dat and written to <AED_initcond|AED2_initcond>/<var>_ini.dat. NULL (default) leaves water quality initial values unchanged. Requires a Simstrat-AED or Simstrat-AED2 configuration (an aed.nml/aed2.nml in path_simstrat).

Value

invisibly, the updated initial conditions data.frame

Details

The existing profile depths (and U, V, k, eps columns) in InitialConditions.dat are left unchanged – temp/salt/wq_init values are recycled (via rep_len()) across however many depths are already defined.

Water quality initial conditions in Simstrat-AED/AED2 follow a two-layer scheme: the aed.nml/aed2.nml <var>_initial field is a fallback constant used for every grid cell, and an optional per-variable <path_aed_initial>/<var>_ini.dat (depth, value) profile – if present – overrides it, interpolated onto the vertical grid. wq_init writes this override file directly (it takes precedence over the nml default regardless of the nml value), rather than editing the nml fallback. Which coupler is in use (Simstrat-AED vs Simstrat-AED2, and therefore the AED_initcond//AED2_initcond/ directory and variable-naming convention) is detected from whichever of aed.nml/aed2.nml exists in path_simstrat.

Examples

if (FALSE) { # \dontrun{
set_simstrat_init(path_simstrat, temp = seq(20, 10, length.out = 10))
set_simstrat_init(path_simstrat, wq_init = list(NIT_amm = 0.5, CHM_oxy = 300))
} # }